Today I and my collaborators have a new paper published in PNAS! Justin Tackney, the lead author of the paper, was kind enough to write up a summary of the findings to publish here on Violent Metaphors. Here is his take:
The genetic characterization of the ancestral population in Beringia for the initial peopling event into North and South America has been limited by the lack of human remains buried at the right time and place. We report on two mitochondrial genomes (mitogenomes) from the Upward Sun River site in Alaska dated to about 11,500 years ago. This site is located in what was then eastern Beringia, and was occupied only a few thousand years after the main migration south, through an inland route, along the pacific coast, or both, about 15,000 years ago. The populations living at Upward Sun River at that time might represent a residual group that subsequently left or disappeared from the region today.
With the permission and support of the Healy Lake Tribal Council and Tanana Chiefs Conference, we obtained DNA from the remains of two individuals buried at the site. One was an infant just a few weeks old. The other was a late pre-term fetus.
While the two remains were initially believed by archaeologists to be maternally related, the infant and the pre-term fetus carried two different mitochondrial ‘haplotypes’, or mitochondrial DNA variants. This is significant because mitochondrial DNA is only maternally inherited, so it means that they did not share a mother. Both haplotypes, C1b and B2, are rare or absent in Northern North America today (although Jennifer, Dennis, and I did find B2 present in a ~1000 YBP population from the Brooks River area of the Alaska Peninsula in a previous paper*, suggesting that it was once more common in Alaska) and both were determined to be phylogenetically within or near the roots of their respective clades.
That these haplotypes were so far north at this very early date supports the Beringian Standstill Hypothesis (the idea that people lived in Beringia for at least several thousand years before moving southward into the Americas) by providing evidence for the ancestral root variants in the initial source population and by showing large genetic variation even within one residential complex. There was a third cremated 3-year old child found above the burial, dated to about the same time as the two human remains analyzed, but the cremation seems to have prevented the preservation of any DNA.
We were able to use the two precisely dated remains to inform the rate of the molecular clock within these two lineages and re-date the time to most recent common ancestor for all known Native American variants within these haplotypes. Our dates were on the younger side of recent estimates for these two clades (C1 and B2), but were close to previous dates calculated with a molecular clock also estimated with ancient DNA. We estimated C1b to coalesce at 12,854 (11,853-14,079) years before present and B2 to coalesce at 12,024 (11,500-14,085) years before present. These younger coalescence dates might be used to support a much shorter period of isolation in Beringia, as suggested by Raghavan and colleagues** earlier this year.
Our two mitogenomes are only the 8th and 9th mitochondrial lineages determined from human remains in the Americas dating to greater than 8,000 years ago and we are one of only 3 sites where the whole mitochondrial genome was sequenced completely. The two individuals at Upward Sun River are the farthest north human remains thus far discovered.
We performed hybridization capture for mitochondrial DNA molecules and then sequenced the captured ancient DNA on an Ion Proton system; we are one of the first groups in our field to use Ion technology for this purpose.
Do you have any questions for the research team? Leave them in the comments below, and either Jennifer or Justin will answer them.
*Raff JA, Tackney JT, O’Rourke DH. 2010. South from Alaska: A pilot aDNA study of genetic history on the Alaska Peninsula and the Eastern Aleutians. Human Biology 42 (5-6): 677-693.
**Raghavan et al. 2015. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science DOI: 10.1126/science.aab3884